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The Gut Microbiome can influence the outcome of your clinical trial

FREE test run 16S data processing and analysis Shotgun metagenomic data processing and analysis FMT Biobank Microbiome profiles in clinical trials and drug response Quick Contact The Gut Microbiome can influence the outcome of your clinical trial Let us help you control this variable! Why consider the gut microbiome in phase II and III trials? [...]

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.vc_custom_1419240516480{background-color: #f9f9f9 !important;} The Gut Microbiome can influence the outcome of your clinical trialFREE test run 16S data processing and analysis Shotgun metagenomic data processing and analysis FMT Biobank Microbiome profiles in clinical trials and drug response Quick Contact The Gut Microbiome can influence the outcome of your clinical trial Let us help you control [...]

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Assessing Drug Toxicity in Pre-Clinical In Vivo Studies: Considering the Microbiome

Key terms in microbiome analyses Microbiome profiling software for 16S/18S/ITS rRNA gene data The human microbiota in the healthcare system The human microbiota in drug development Assessing Drug Toxicity in Pre-Clinical In Vivo Studies: Considering the Microbiome Assessing Drug Toxicity in Pre-Clinical In Vivo Studies: Considering the Microbiome Before new medications can be approved for [...]

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The human microbiota in the healthcare system

Key terms in microbiome analyses Microbiome profiling software for 16S/18S/ITS rRNA gene data The human microbiota in the healthcare system The human microbiota in drug development Assessing Drug Toxicity in Pre-Clinical In Vivo Studies: Considering the Microbiome Quick Contact The human microbiota in the healthcare system The inner and outer surfaces of the human body [...]

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The human microbiota in drug development

Key terms in microbiome analyses Microbiome profiling software for 16S/18S/ITS rRNA gene data The human microbiota in the healthcare system The human microbiota in drug development Assessing Drug Toxicity in Pre-Clinical In Vivo Studies: Considering the Microbiome Quick Contact The human microbiota in drug development Incorporating the human gut microbiota in development of pharmacological and [...]

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Biobank

ServicesFREE test run 16S data processing and analysis Shotgun metagenomic data processing and analysis FMT Biobank Microbiome profiles in clinical trials and drug response Biobank The human microbiota plays an essential role for human health and well-being. By offering human fecal samples, we aim to enable and assist active consideration of the human gut microbiome [...]

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Free test run

ServicesFREE test run 16S data processing and analysis Shotgun metagenomic data processing and analysis FMT Biobank Microbiome profiles in clinical trials and drug response Free test run We will analyse a subset of your samples for FREE, provide you with the results, a discussion of the output and let you decide if we are the [...]

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16S data processing and analysis

ServicesFREE test run 16S data processing and analysis Shotgun metagenomic data processing and analysis FMT Biobank Microbiome profiles in clinical trials and drug response 16S data processing and analysis Sequencing of the 16S rRNA gene is commonly used for profiling of the microbiome community in a complex biological sample, such as a fecal sample or [...]

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Shotgun metagenomic data processing and analysis

FREE test run 16S data processing and analysis Shotgun metagenomic data processing and analysis FMT Biobank Microbiome profiles in clinical trials and drug response Quick Contact Shotgun metagenomic data processing and analysis Shotgun metagenomic sequencing provide information on both the relative abundance of microorganisms found in a microbial sample and the functional capacity of the [...]

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Sample Page

This is an example page. It’s different from a blog post because it will stay in one place and will show up in your site navigation (in most themes). Most people start with an About page that introduces them to potential site visitors. It might say something like this: Hi there! I’m a bike messenger […]

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Microbiome profiling software for 16S/18S/ITS rRNA gene dataty

Microbiome profiling of amplicon data is performed using BION where applicable. BION is open-source (with restriction on commercial usage) [BION software] exclusively written by [Danish Genome Institute], Aarhus, Denmark.

 

BION does all the basic processing for amplicon reads: cleaning, joining, filtering, de-replication, clustering, chimera checking and similarity matching, and finally creates organism abundance profiles.

We believe BION is more accurate than other packages. The main reasons for that are:

Better profiling logic.

Similarities are processed by a two-pass logic where highly similar alternative reference taxa are being chosen by their relative similarities.

 

This usually results in reliable mapping at the species level rather than genus, provided the sequences are of a good length and quality.

Cleaner sample data.

Through small tweaks of the logic behind each step, the sequences that reach the similarity mapper have optimal quality.

 

For example the clustering logic prefers the highest quality sequences as cluster center and only these are then similarity-matched.

Cleaner reference data.

We post-process reference data through a number of steps which in combination reduce false positive and negative matches (the “bogusphere”).

 

We plan to harvest and distribute our own reference sequences from the primary databanks in response to growing demand.

Data restrictions: At the moment BION can only process SSU RNA and ITS data, either paired or single.

BION is a software under constant improvement and maintenance, and our close collaboration with the Danish Genome Institute ensures that the software is customized to your specific data. The Danish Genome Institute plan to harvest and distribute their own reference sequences from the primary databanks in response to growing demand, thereby ensuring up-to-date reference data.

To facilitate an open and communicative service, we provide a downloadable [description] of the logic behind all steps, a 1-page feature [summary sheet], a typical [results archive], an [abundance table] in HTML form (made from 16S rRNA V3-V4 samples with known content), and the [whole code archive] for the version currently used in our services.

Free reruns as reference data improves. If your data is of good quality and you let it stay on our servers, then we will rerun it with new methods as they appear, against better reference data as they become available, all at no cost.

The NGS-based microbiome field is in early stages and new organisms are constantly identified and/or known organisms are regrouped.

 

As a consequence, it can often be meaningful to re-analyse  data at later time points.  In exchange for the free re-runs, you allow us to make internal use of this (anonymized) data as a way to improve our service for other clients.

Local installation of the BION software

In addition to our online service for data processing and analysis, we offer to support you with a local installation of the BION package into your existing infrastructure. This option may be ideal if you routinely work with amplicon data and would like to process the data in-house, without having to deal with software installation or maintenance.

 

We offer to help with the installation (remotely through screensharing and Skype communication) and then help to write a workflow “guide” that fits your input data and get the first data through. The local installation is offered via The Danish Genome Institute , who also have service subscriptions for those who want our help any time needed.